NPASS Compound

Natural Product: NPC609111

Natural Product ID	NPC609111
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZCPYJMSBMMBYSS-LLVKDONJSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL5178107
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 36 37 0 0 0 0 0 0 0 0999 V2000 4.2778 1.5146 0.2491 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4534 0.0291 0.0282 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5687 -0.4174 -1.1152 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1032 -0.1528 -0.8434 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6067 -0.8624 0.3739 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1605 -0.5472 0.5746 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7424 -0.9400 -0.5354 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1364 -0.5381 -0.2363 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1988 -1.3211 -0.6965 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4798 -0.9088 -0.4374 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5423 -1.6838 -0.8928 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7333 0.2353 0.2514 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6796 0.9980 0.7003 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8702 2.1836 1.4134 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3690 0.6150 0.4593 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2472 1.3977 0.9631 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4519 2.4429 1.5894 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0547 0.8960 0.6950 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8890 1.7081 1.2878 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2548 2.0547 0.2087 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6368 1.9715 -0.5105 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4998 -0.1371 -0.3014 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2125 -0.5253 0.9443 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8474 0.1910 -2.0002 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7212 -1.4773 -1.3702 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9020 0.9317 -0.7763 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5696 -0.5195 -1.7555 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1824 -0.5444 1.2679 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7285 -1.9643 0.2558 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1818 -0.9722 1.5557 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4226 -0.3442 -1.4389 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6656 -2.0089 -0.8231 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9628 -2.2312 -1.2448 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8498 -2.5101 -0.4321 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7526 0.5272 0.4352 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3829 2.9098 0.9329 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 10 12 2 0 12 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 6 1 0 15 8 1 0 1 19 1 0 1 20 1 0 1 21 1 0 2 22 1 0 2 23 1 0 3 24 1 0 3 25 1 0 4 26 1 0 4 27 1 0 5 28 1 0 5 29 1 0 6 30 1 1 7 31 1 0 7 32 1 0 9 33 1 0 11 34 1 0 12 35 1 0 14 36 1 0 M END

Standard InCHIKey	ZCPYJMSBMMBYSS-LLVKDONJSA-N
Standard InCHI	InChI=1S/C14H18O4/c1-2-3-4-5-11-7-9-6-10(15)8-12(16)13(9)14(17)18-11/h6,8,11,15-16H,2-5,7H2,1H3/t11-/m1/s1
SMILES	CCCCC[C@@H]1Cc2cc(O)cc(O)c2C(=O)O1

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO62265	Penicillium simplicissimum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO61791	Penicillium simplicissimum MA-332	Genus	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC609111 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	14707
0.1-0.2	32167
0.2-0.3	2744
0.3-0.4	168
0.4-0.5	38
0.5-0.6	24
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.74	Intermediate Similarity	NPC53649
0.717	Intermediate Similarity	NPC472602
0.6977	Remote Similarity	NPC235115
0.6875	Remote Similarity	NPC600571
0.6792	Remote Similarity	NPC764
0.6735	Remote Similarity	NPC159721
0.6481	Remote Similarity	NPC487444
0.6458	Remote Similarity	NPC472600
0.6275	Remote Similarity	NPC70380
0.5926	Remote Similarity	NPC487947
0.5818	Remote Similarity	NPC608268
0.5769	Remote Similarity	NPC27407
0.566	Remote Similarity	NPC472603
0.5556	Remote Similarity	NPC142027
0.5556	Remote Similarity	NPC472604
0.5532	Remote Similarity	NPC219892
0.5517	Remote Similarity	NPC472035
0.5455	Remote Similarity	NPC42540
0.5439	Remote Similarity	NPC191835
0.5439	Remote Similarity	NPC609527
0.5439	Remote Similarity	NPC610163
0.5439	Remote Similarity	NPC611086
0.5424	Remote Similarity	NPC481134
0.537	Remote Similarity	NPC472605
0.5345	Remote Similarity	NPC212693
0.5345	Remote Similarity	NPC94248
0.5254	Remote Similarity	NPC609495
0.5246	Remote Similarity	NPC126882
0.5179	Remote Similarity	NPC105456
0.5179	Remote Similarity	NPC139634
0.5094	Remote Similarity	NPC487604
0.5088	Remote Similarity	NPC151607
0.5088	Remote Similarity	NPC609639

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC609111 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3933
0.1-0.2	5099
0.2-0.3	114
0.3-0.4	4
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data